No-tillage and straw returning are important practices for preserving and improving soil quality for the sustainable management system. The experimental field was established in 2007 with conventional tillage (CT), conventional tillage with straw returning (CTS), no-tillage (NT), and no-tillage with straw returning (NTS) practice in rice (Oryza sativa L.)-rape (Brassica napus L.) cropping system. The soil samples were collected in 2013-2015 from 0-20 and 20-40 cm depth to investigate the effects on soil organic C (SOC), water-stable aggregation (> 5, 5-2, 2-1, 1.0-0.5, 0.25-0.5, and < 0.25 mm), and their stability in paddy soil of the central China. In the last year (2015), the integrative use of no-tillage and straw returning significantly increased SOC content and contribution of the macroaggregates in 0-20 cm and microaggregates in 20-40 cm depth. Compared with CT, SOC content, mean weight diameter (MWD), geometric mean diameter (GMD), and fractal dimensions (FD) under NTS were increased 25%, 21%, 19%, and 12%, respectively, in the 0-20 cm depth. In 20-40 cm depth, the soil micro-aggregates were higher under CTS treatment. Percentages of macroaggregates and microaggregates under NTS were increased 60% and 40% in the 0-20 cm depth. The SOC had positive linear relationship with MWD, GMD, > 5, 2-5, 1-2, and 0.25-0.5 mm aggregates. Thus, long-term combine use of NT with straw returning practices significantly improved SOC and water-stable aggregation. No-tillage and straw returning appeared to be promising and sustainable strategies to conserve SOC sequestration and stable soil aggregates in rice-rape cropping system.